text: This article aims at demonstrating the relevance of developing novel methods to study molecular regulatory networks. Two examples of molecular tools enabling the manipulation of protein interactions are described. CIDs (chemical inducers of dimerization) are derivatives of immunophilin ligands, such as FK506 or cyclosporin A. Their use offers a fine control of dimerization or relocation of chimeric proteins expressed in living cells or in animals. Future generations of CIDs should act on native proteins. Peptide aptamers are artificial proteins selected to bind protein targets within living cells or for conferring particular phenotypes. These molecules show a high interaction specificity and a good binding affinity, allowing them to inhibit in vivo some functions of their target by disrupting specific interactions. Manipulations on protein interactions should facilitate the study of regulatory networks but could also inspire novel therapeutic strategies.